In this study the ecology, biology and classification of the sea cucumber species of the Red Sea coast of Egypt and Gulf of Aqaba were examined in order to resolve some of the long standing question on the identification and classification of sea cucumber.The introduction of the new barcoding technique as a tool for sea cucumber identification was also tested in this study in order to assess its accuracy and potential of the technique in identifying sea cucumber individuals. A total of 18 different (species) of sea cucumber were collected from the Egyptian coast and examined for both morphological and molecular characteristics. One new species of sea cucumber were identified from the Egyptian coast of the Red Sea (Actinopyga.sp.nov). Cryptic species complex were also identified for the Holothuria atra population in the Red Sea using the molecular analysis of the mitochondrial COI gene.In this study another experiment were conducted in order to identify sea cucumber species from cooked or dried materials using the molecular techniques. As well as testing the possibility of using the DNA barcoding technique in order to identify badly/long period preserved museum specimens in order to try to identify the unknown specimens in the natural history museums around the globe.The use of the molecular DNA barcoding technique proves to be a good reliable method for sea cucumber ID; the technique was capable of resolving some of the standing taxonomic problems including the Holothuria fuscogilva /Holothuria nobilis species complex and the Pearsonthuria graeffei. The results also raised some questions about the classification of the genus Bohadchia and the Actinopyga crassa species in the Red Sea.